Carbohydrates can be envisioned as the K'nex™ toys of life. They are building blocks with multiple points of attachment, which can form highly branched and stereochemically-rich structures. They are difficult to study because the connecting points are not as sturdy as the K'nex. In fact, the binding force is very weak compared to the binding force of an antigen or antibody. The affinities, i.e., the force of attraction between molecules, of the latter can be 103-109 greater. Therefore, it is very difficult to synthesize a sufficient quantity of a carbohydrate for lab analysis. Traditionally it may take a day or more to measure a single carbohydrate-protein interaction using compounds in microgram to milligram amounts.
Carbohydrates, present as free oligosaccharides or as glycoconjugates, play an important role in many biological events, particularly those involving cell surfaces. Specific interactions between carbohydrates and proteins are often essential in viral and bacterial infection, the immune response, differentiation and development, and the progression of tumor cell metastasis. Therefore an understanding of carbohydrate-protein interactions at the molecular level would lead to a better insight into the biological process of living systems and assist the development of therapeutic and diagnostic strategies.
Despite the ubiquity and importance of carbohydrates in biology, difficulties in the study of carbohydrate-protein interactions have hindered the development of a mechanistic understanding of carbohydrate structure and function. The structural complexity of carbohydrates is a major obstacle: while the other two classes of biopolymers, nucleic acid and proteins, have a linear arrangement of repeating units, carbohydrate building blocks have multiple points of attachment, leading to highly branched and stereochemically-rich structures. In addition, binding affinities are weak typically in the ˜10−3-10−6 M range of dissociation constants, compared with antigen-antibody interactions (10−8-10−12). While techniques such as isothermal titration calorimetry (ITC), affinity capillary electrophoresis, surface plasmon resonance (SPR), and frontal affinity chromatography are all significant advances, they are often limited by the amount of available materials. Hence, the design of sensitive and high throughput technologies for characterizing carbohydrate-protein interactions remain a challenge.
However, little attention has been paid to the systematic kinetic and thermodynamic investigation of the interactions using glycan microarrays. Recently, MacBeath et al. reported a quantitative analysis of protein-peptide interactions using a protein microarray; in this work the interactions of Src homology 2 and the phosphotyrosine binding domain of phosphopeptides were measured, and this study provided a better understanding of the tyrosine phosphorylation network for the epidermal growth factor receptor.